CalculateDHI: Calculate DHI value for drug MSI data

In pietrofranceschi/HomogenMSI: Calculate drug homogeneity value for MSI data

Description

This function calculates the DHI value for the drug image extracted from MSI data.

Usage

CalculateDHI(drugImg,Nu=1,QuantLevel=NULL,maskImg=NULL)

Arguments

drugImg	Input matrix containing the pixel intensities
maskImg	Matrix identifying the pixels belonging to the tissue (1 tissue, 0 background). It must have the same size as drugImg
QuantLevel	Maximum possible gray-levels in drug ion image. default = 0, i.e., original image
Nu	Lowest size-zone value used for DHI calculation. default = 1

Details

The algorithm is based on the following workflow:

1. Derive new quantized drug image at user-defined qunatization value.

2. Derive gray-level size-zone matrix (GLSZM) for new drug quantized image (default value =0).

3. Derive homogeneous size-zone value from GLSZM at user-defined Nu value (default value =1).

4. Normalized overall value with complete tumor area which is obtained from tumor mask file.

Value

DHI value for given drug ms file

Author(s)

Mridula Prasad [e-mail]

References

https://github.com/pietrofranceschi/HomogenMSI

Examples

## load package
library(HomogenMSI)
data("DHIimages")

## Input drug and mask images

drugImg = DHIimages[[20]]
maskImg = DHIimages[[1]]
maskImg[maskImg !=0] =1

#Calculate DHI with default input parameters
print(CalculateDHI(drugImg,maskImg=maskImg))

# calculate DHI with user-defined Nu value
print(CalculateDHI(drugImg,maskImg=maskImg,QuantLevel=0,Nu=5))

pietrofranceschi/HomogenMSI documentation built on May 21, 2019, 9:22 a.m.